Most income for large alliances comes from mining moons and from taxes on members' income. Ships lost in these alliance-level battles are usually (at least partially) reimbursed by the alliance.

Incidentally, this is what makes some territory more valuable to hold for an alliance, and worth fighting over - some areas can generate much more income than others. Most of the high-level metagame happens over who controls what moons, which is actually invisible to the average player.